How to control the spatial distribution of nanoparticles to meet different performance requirements is a constant challenge in the field of polymer nanocomposites. Current studies have been focused on the flexible polymer chain systems. In this study, the rigid polyimide (PI) chain grafted silica particles with different grafting chain lengths and grafting densities were prepared by “grafting to” method, and the influence of polymerization degree of grafted chains (N), matrix chains (P), and grafting density (σ) on the spatial distribution of nanoparticles in the PI matrix was explored. The glass transition temperature (Tg) of PI composites was systematically investigated as well. The results show that silica particles are well dispersed in polyamic acid composite systems, while aggregation and small clusters appear in PI nanocomposites after thermal imidization. Besides, the particle size has no impact on the spatial distribution of nanoparticles. When σ·N0.5 ≪ (N/P)2, the grafted and matrix chains interpenetrate, and the frictional resistance of the segment increases, resulting in restricted relaxation kinetics and Tg increase of the PI composite system. In addition, smaller particle size and longer grafted chains are beneficial to improving Tg of composites. These results are all propitious to complete the microstructure control theory of nanocomposites and make a theoretical foundation for the high performance and multi-function of PI nanocomposites.